FHIR Osiris Implementation Guide
2.1.0 - ci-build
FHIR Osiris Implementation Guide
2.1.0 - ci-build
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| Official URL: https://build.fhir.org/ig/arkhn/arkhn-ig-osiris/StructureDefinition/copy-number | Version: 2.1.0 | |||
| Active as of 2023-04-10 | Computable Name: CopyNumber | |||
Observation of a Copy Number variant derived from a SequencingAnalysis. The CopyNumber profile is used to indicate the pathogenicity, the actionability, the loss of heterozygosity, the cytogenetic location, the start - end positions, the reference sequence assembly, the variation code, the segment intensity, the number of copy found and the Copy Number segment size.
Usage:
Description of Profiles, Differentials, Snapshots and how the different presentations work.
This structure is derived from Variant
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
  Observation | 0..* | Variant | Variant | |
  subject | 0..1 | Reference(Oncology Patient) | Who and/or what the observation is about | |
  Slices for derivedFrom | 1..* | Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) | Related measurements the observation is made from Slice: Unordered, Open by pattern:reference | |
   derivedFrom:Analysis | 1..1 | Reference(Sequencing Analysis) | Analysis from which come this observation | |
| component:cytogenetic-location | 0..* | BackboneElement | Cytogenetic (chromosome) location | |
 component:ref-sequence-assembly | 0..* | BackboneElement | Human reference sequence assembly version | |
   valueCodeableConcept | 1..1 | CodeableConcept | Actual component result | |
| component:variation-code | 0..1 | BackboneElement | Variation Code | |
| valueCodeableConcept | 1..1 | CodeableConcept | Actual component result | |
| component:copy-number | 0..1 | BackboneElement | Genomic structural variant copy number | |
| valueQuantity | 1..1 | Count | A measured or measurable amount | |
| component:exact-start-end | 0..1 | BackboneElement | Exact start-end | |
 valueRange | 1..1 | Range | Actual component result | |
| low | 1..1 | SimpleQuantity | Exact Start | |
 high | 0..1 | SimpleQuantity | Exact End | |
| component:variant-length | 0..1 | BackboneElement | Structural variant length | |
| component:actionability | 0..1 | BackboneElement | Conclusion of the clinicians wether the variant is actionable or not during the Molecular Tumor Board | |
 code | 1..1 | CodeableConcept | Type of component observation (code / type) Required Pattern: At least the following | |
  coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 93348-1 | |
 value[x] | 0..1 | boolean | Actual component result Slice: Unordered, Open by type:$this | |
| valueBoolean | 0..1 | boolean | Actual component result | |
| component:proposed-for-orientation | 0..1 | BackboneElement | Is the ClinicalTumorBoardConclusion used to orient the treatment decision ? | |
| code | 1..1 | CodeableConcept | Type of component observation (code / type) Required Pattern: At least the following | |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/umls | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: C0449889 | |
| value[x] | 0..1 | boolean | Actual component result Slice: Unordered, Open by type:$this | |
| valueBoolean | 0..1 | boolean | Actual component result | |
| component:pathogenicity | 0..1 | BackboneElement | Conclusion of the biologist on the pathogenicity of the variant before the Molecular Tumor Board | |
| code | 1..1 | CodeableConcept | Type of component observation (code / type) Required Pattern: At least the following | |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 74019-1 | |
| value[x] | 0..1 | CodeableConcept | Actual component result Slice: Unordered, Open by type:$this Binding: Pathogenicity Value Set (required) | |
| valueCodeableConcept | 0..1 | CodeableConcept | Actual component result | |
| component:loss-of-heterozygosity | 0..1 | BackboneElement | Is the segment located in a region of loss of heterozygosity ? (can be independant from copy number information | |
| code | 1..1 | CodeableConcept | Type of component observation (code / type) Required Pattern: At least the following | |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/umls | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: C1881449 | |
| value[x] | 0..1 | boolean | Actual component result Slice: Unordered, Open by type:$this | |
| valueBoolean | 0..1 | boolean | Actual component result | |
 component:segment-intensity | 0..1 | BackboneElement | Intensity of the measured signal | |
| code | 1..1 | CodeableConcept | Type of component observation (code / type) Required Pattern: At least the following | |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/umls | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: C2732930 | |
| value[x] | 0..1 | integer | Actual component result Slice: Unordered, Open by type:$this | |
| valueInteger | 0..1 | integer | Actual component result | |
| Documentation for this format | ||||
| Path | Conformance | ValueSet |
| Observation.component:pathogenicity.value[x] | required | Pathogenicity |
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
| Observation | C | 0..* | Variant | Variant |
 implicitRules | ?!Σ | 0..1 | uri | A set of rules under which this content was created |
| BodyStructure | 0..1 | Reference(BodyStructure) | Target anatomic location or structure URL: http://hl7.org/fhir/StructureDefinition/bodySite | |
| SecondaryFinding | 0..1 | CodeableConcept | Secondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement.
For more detail, please see:
https://ghr.nlm.nih.gov/primer/testing/secondaryfindings URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding Binding: ObservationCategoryCodes (extensible): Codes to denote a guideline or policy statement.when a genetic test result is being shared as a secondary finding. | |
 modifierExtension | ?! | 0..* | Extension | Extensions that cannot be ignored |
| status | ?!Σ | 1..1 | code | registered | preliminary | final | amended + Binding: ObservationStatus (required): Codes providing the status of an observation. |
  category | 1..* | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. Required Pattern: At least the following | |
 coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: laboratory | |
| code | Σ | 1..1 | CodeableConcept | Genetic variant assessment Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 69548-6 | |
| subject | Σ | 0..1 | Reference(Oncology Patient) | Who and/or what the observation is about |
| Slices for effective[x] | Σ | 0..1 | dateTime | Clinically relevant time/time-period for observation Slice: Unordered, Closed by type:$this |
 effective[x]:effectiveDateTime | Σ | 0..1 | dateTime | Clinically relevant time/time-period for observation |
| performer | Σ | 0..1 | Reference(Practitioner | Organization | Patient | RelatedPerson) | Who is responsible for the observation |
| value[x] | ΣC | 1..1 | CodeableConcept | Present|Absent|No call|Indeterminate Binding: LOINC Answer List LL1971-2 (required): Genetic Variant Assessment |
| Slices for derivedFrom | Σ | 1..* | Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) | Related measurements the observation is made from Slice: Unordered, Open by pattern:reference |
| derivedFrom:Analysis | Σ | 1..1 | Reference(Sequencing Analysis) | Analysis from which come this observation |
| Slices for component | Σ | 0..* | BackboneElement | Component results Slice: Unordered, Open by pattern:code |
| component:All Slices | Content/Rules for all slices | |||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. |
| component:gene-studied | Σ | 0..* | BackboneElement | Gene studied ID |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48018-6 | |
| value[x] | Σ | 1..1 | CodeableConcept | If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used. Binding: HGNC (extensible): HGNC: Human Gene Nomenclature Committee |
| component:cytogenetic-location | Σ | 0..* | BackboneElement | Cytogenetic (chromosome) location |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48001-2 | |
| value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding: (unbound) (example): Binding not yet defined |
| component:ref-sequence-assembly | Σ | 0..* | BackboneElement | Human reference sequence assembly version |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 62374-4 | |
| value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding: LOINC Answer List LL1040-6 (extensible): Human reference sequence NCBI build IDs |
| component:dna-chg | Σ | 0..1 | BackboneElement | DNA Change - Transcript (cHGVS) |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48004-6 | |
| value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding: HGVS (required): HGVS: Sequence Variant Nomenclature from the Human Genome Variation Society |
| component:dna-chg-type | Σ | 0..1 | BackboneElement | DNA change type |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48019-4 | |
| value[x] | Σ | 1..1 | CodeableConcept | Concepts in sequence ontology under SO:0002072 (see http://www.sequenceontology.org/browser/current_release/term/SO:0002072) Binding: DNA Change Type (extensible): DNA Change type values (Sequence Ontology) |
| component:functional-annotation | Σ | 0..* | BackboneElement | Functional Annotation |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: functional-annotation | |
| value[x] | Σ | 1..1 | CodeableConcept | Concepts in sequence ontology under SO:0001537 (see http://www.sequenceontology.org/browser/current_release/term/SO:0001537) Binding: Functional Annotation (extensible): Functional Annotation (Sequence Ontology) |
| component:variation-code | Σ | 0..1 | BackboneElement | Variation Code |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81252-9 | |
| value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding: (unbound) (example): Binding not yet defined |
| component:dbSNP-id | Σ | 0..1 | BackboneElement | dbSNP ID |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81255-2 | |
| value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding: (unbound) (example): Binding not yet defined |
| component:genomic-dna-chg | Σ | 0..1 | BackboneElement | DNA Change - Genomic (gHGVS) |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81290-9 | |
| value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding: HGVS (required): HGVS: Sequence Variant Nomenclature from the Human Genome Variation Society |
| component:genomic-source-class | Σ | 0..1 | BackboneElement | Genomic source class |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48002-0 | |
| value[x] | Σ | 1..1 | CodeableConcept | Germline | Somatic | Fetal | Likely germline | Likely somatic |Likely fetal | Unknown genomic origin | De novo Binding: LOINC Answer List LL378-1 (extensible): Genomic source class values |
| component:amino-acid-chg | Σ | 0..1 | BackboneElement | Amino acid change (pHGVS) |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48005-3 | |
| value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding: HGVS (required): HGVS: Sequence Variant Nomenclature from the Human Genome Variation Society |
| component:amino-acid-chg-type | Σ | 0..1 | BackboneElement | Amino acid change type |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48006-1 | |
| value[x] | Σ | 1..1 | CodeableConcept | Wild type | Deletion | Duplication | Frameshift | Initiating Methionine | Insertion | Insertion and Deletion | Missense | Silent | Stop Codon Mutation Binding: LOINC Answer List LL380-7 (required): Amino acid change type values |
| component:transcript-ref-seq | Σ | 0..1 | BackboneElement | Transcript reference sequence ID |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 51958-7 | |
| value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding: (unbound) (example): Binding not yet defined |
| component:genomic-ref-seq | Σ | 0..1 | BackboneElement | Genomic reference sequence ID |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48013-7 | |
| value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding: (unbound) (example): Binding not yet defined |
| component:sample-allelic-frequency | Σ | 0..1 | BackboneElement | Sample Allelic Frequency |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Sample Sample VAF Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81258-6 | |
| value[x] | Σ | 1..1 | Quantity | Actual component result |
| value | Σ | 1..1 | decimal | Numerical value (with implicit precision) |
| comparator | ?!Σ | 0..1 | code | < | <= | >= | > - how to understand the value Binding: QuantityComparator (required): How the Quantity should be understood and represented. |
| system | ΣC | 1..1 | uri | System that defines coded unit form Fixed Value: http://unitsofmeasure.org |
| component:allelic-read-depth | Σ | 0..* | BackboneElement | Allelic read depth |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 82121-5 | |
| value[x] | Σ | 1..1 | Quantity | Actual component result |
| component:allelic-state | Σ | 0..1 | BackboneElement | Allelic state |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 53034-5 | |
| value[x] | Σ | 1..1 | CodeableConcept | Heteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous Binding: LOINC Answer List LL381-5 (extensible): Allelic state type values |
| component:copy-number | Σ | 0..1 | BackboneElement | Genomic structural variant copy number |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 82155-3 | |
| value[x] | C | 1..1 | Count | A measured or measurable amount |
| component:ref-allele | Σ | 0..1 | BackboneElement | Genomic ref allele |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 69547-8 | |
| value[x] | Σ | 1..1 | string | Actual component result |
| component:alt-allele | Σ | 0..1 | BackboneElement | Genomic alt allele |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 69551-0 | |
| value[x] | Σ | 1..1 | string | Actual component result |
| component:coordinate-system | Σ | 0..1 | BackboneElement | Coordinate System |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 92822-6 | |
| value[x] | Σ | 1..1 | CodeableConcept | 0-based interval | 0-based character | 1-based character Binding: LOINC Answer List LL5323-2 (preferred): Base coordinate systems start and end measurements for variants |
| component:exact-start-end | Σ | 0..1 | BackboneElement | Exact start-end |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: exact-start-end | |
| value[x] | Σ | 1..1 | Range | Actual component result |
| low | Σ | 1..1 | SimpleQuantity | Exact Start |
| component:variant-length | Σ | 0..1 | BackboneElement | Structural variant length |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81300-6 | |
| value[x] | C | 1..1 | Count | A measured or measurable amount |
| component:outer-start-end | Σ | 0..1 | BackboneElement | Variant outer start and end |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: outer-start-end | |
| value[x] | Σ | 1..1 | Range | Actual component result |
| low | Σ | 1..1 | SimpleQuantity | Low limit |
| high | Σ | 1..1 | SimpleQuantity | High limit |
| component:inner-start-end | Σ | 0..1 | BackboneElement | Variant inner start and end |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: inner-start-end | |
| value[x] | Σ | 1..1 | Range | Actual component result |
| low | Σ | 1..1 | SimpleQuantity | Low limit |
| high | Σ | 1..1 | SimpleQuantity | High limit |
| component:chromosome-copy-number-change-type | Σ | 0..1 | BackboneElement | Chromosome copy number change type |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 62378-5 | |
| value[x] | Σ | 1..1 | CodeableConcept | Copy number gain | Copy number loss Binding: LOINC Answer List LL1041-4 (required): Copy Number Change Types |
| component:arrCGH-ratio | Σ | 0..1 | BackboneElement | Structural variant reported arrCGH [Ratio] |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81299-0 | |
| value[x] | C | 1..1 | SimpleQuantity | A fixed quantity (no comparator) |
| component:complex-var-type | Σ | 0..1 | BackboneElement | Complex variant type |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81263-6 | |
| value[x] | Σ | 1..1 | CodeableConcept | Compound heterozygous | Double heterozygous | Haplotype | Hemizygous Binding: LOINC Answer List LL3999-1 (required): Complex variant type |
| component:cytogenomic-nomenclature | Σ | 0..1 | BackboneElement | Cytogenomic Nomenclature |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Variant ISCN Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81291-7 | |
| value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding: (unbound) (example): Binding not yet defined |
| component:variant-inheritance | Σ | 0..1 | BackboneElement | Variant Inheritance |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: variant-inheritance | |
| value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding: Variant Inheritance (extensible): Variant Inheritance (Sequence Ontology) |
| component:actionability | Σ | 0..1 | BackboneElement | Conclusion of the clinicians wether the variant is actionable or not during the Molecular Tumor Board |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 93348-1 | |
| Slices for value[x] | Σ | 0..1 | boolean | Actual component result Slice: Unordered, Closed by type:$this |
| value[x]:valueBoolean | Σ | 0..1 | boolean | Actual component result |
| component:proposed-for-orientation | Σ | 0..1 | BackboneElement | Is the ClinicalTumorBoardConclusion used to orient the treatment decision ? |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/umls | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: C0449889 | |
| Slices for value[x] | Σ | 0..1 | boolean | Actual component result Slice: Unordered, Closed by type:$this |
| value[x]:valueBoolean | Σ | 0..1 | boolean | Actual component result |
| component:pathogenicity | Σ | 0..1 | BackboneElement | Conclusion of the biologist on the pathogenicity of the variant before the Molecular Tumor Board |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 74019-1 | |
| Slices for value[x] | Σ | 0..1 | CodeableConcept | Actual component result Slice: Unordered, Closed by type:$this Binding: Pathogenicity Value Set (required) |
| value[x]:valueCodeableConcept | Σ | 0..1 | CodeableConcept | Actual component result |
| component:loss-of-heterozygosity | Σ | 0..1 | BackboneElement | Is the segment located in a region of loss of heterozygosity ? (can be independant from copy number information |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/umls | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: C1881449 | |
| Slices for value[x] | Σ | 0..1 | boolean | Actual component result Slice: Unordered, Closed by type:$this |
| value[x]:valueBoolean | Σ | 0..1 | boolean | Actual component result |
| component:segment-intensity | Σ | 0..1 | BackboneElement | Intensity of the measured signal |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/umls | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: C2732930 | |
| Slices for value[x] | Σ | 0..1 | integer | Actual component result Slice: Unordered, Closed by type:$this |
| value[x]:valueInteger | Σ | 0..1 | integer | Actual component result |
| Documentation for this format | ||||
| Path | Conformance | ValueSet / Code |
| Observation.status | required | ObservationStatus |
| Observation.category | preferred | Pattern: laboratory |
| Observation.code | example | Pattern: LOINC code 69548-6 |
| Observation.value[x] | required | LOINC LL1971-2 |
| Observation.component.code | example | LOINCCodes (a valid code from LOINC) |
| Observation.component:gene-studied.code | example | Pattern: LOINC code 48018-6 |
| Observation.component:gene-studied.value[x] | extensible | HGNC |
| Observation.component:cytogenetic-location.code | example | Pattern: LOINC code 48001-2 |
| Observation.component:cytogenetic-location.value[x] | example | |
| Observation.component:ref-sequence-assembly.code | example | Pattern: LOINC code 62374-4 |
| Observation.component:ref-sequence-assembly.value[x] | extensible | LOINC LL1040-6 |
| Observation.component:dna-chg.code | example | Pattern: LOINC code 48004-6 |
| Observation.component:dna-chg.value[x] | required | HGVS |
| Observation.component:dna-chg-type.code | example | Pattern: LOINC code 48019-4 |
| Observation.component:dna-chg-type.value[x] | extensible | DnaChangeType |
| Observation.component:functional-annotation.code | example | Pattern: functional-annotation |
| Observation.component:functional-annotation.value[x] | extensible | FunctionalAnnotation |
| Observation.component:variation-code.code | example | Pattern: LOINC code 81252-9 |
| Observation.component:variation-code.value[x] | example | |
| Observation.component:dbSNP-id.code | example | Pattern: LOINC code 81255-2 |
| Observation.component:dbSNP-id.value[x] | example | |
| Observation.component:genomic-dna-chg.code | example | Pattern: LOINC code 81290-9 |
| Observation.component:genomic-dna-chg.value[x] | required | HGVS |
| Observation.component:genomic-source-class.code | example | Pattern: LOINC code 48002-0 |
| Observation.component:genomic-source-class.value[x] | extensible | LOINC LL378-1 |
| Observation.component:amino-acid-chg.code | example | Pattern: LOINC code 48005-3 |
| Observation.component:amino-acid-chg.value[x] | required | HGVS |
| Observation.component:amino-acid-chg-type.code | example | Pattern: LOINC code 48006-1 |
| Observation.component:amino-acid-chg-type.value[x] | required | LOINC LL380-7 |
| Observation.component:transcript-ref-seq.code | example | Pattern: LOINC code 51958-7 |
| Observation.component:transcript-ref-seq.value[x] | example | |
| Observation.component:genomic-ref-seq.code | example | Pattern: LOINC code 48013-7 |
| Observation.component:genomic-ref-seq.value[x] | example | |
| Observation.component:sample-allelic-frequency.code | example | Pattern: LOINC code 81258-6 |
| Observation.component:sample-allelic-frequency.value[x].comparator | required | QuantityComparator |
| Observation.component:allelic-read-depth.code | example | Pattern: LOINC code 82121-5 |
| Observation.component:allelic-state.code | example | Pattern: LOINC code 53034-5 |
| Observation.component:allelic-state.value[x] | extensible | LOINC LL381-5 |
| Observation.component:copy-number.code | example | Pattern: LOINC code 82155-3 |
| Observation.component:ref-allele.code | example | Pattern: LOINC code 69547-8 |
| Observation.component:alt-allele.code | example | Pattern: LOINC code 69551-0 |
| Observation.component:coordinate-system.code | example | Pattern: LOINC code 92822-6 |
| Observation.component:coordinate-system.value[x] | preferred | LOINC LL5323-2 |
| Observation.component:exact-start-end.code | example | Pattern: exact-start-end |
| Observation.component:variant-length.code | example | Pattern: LOINC code 81300-6 |
| Observation.component:outer-start-end.code | example | Pattern: outer-start-end |
| Observation.component:inner-start-end.code | example | Pattern: inner-start-end |
| Observation.component:chromosome-copy-number-change-type.code | example | Pattern: LOINC code 62378-5 |
| Observation.component:chromosome-copy-number-change-type.value[x] | required | LOINC LL1041-4 |
| Observation.component:arrCGH-ratio.code | example | Pattern: LOINC code 81299-0 |
| Observation.component:complex-var-type.code | example | Pattern: LOINC code 81263-6 |
| Observation.component:complex-var-type.value[x] | required | LOINC LL3999-1 |
| Observation.component:cytogenomic-nomenclature.code | example | Pattern: LOINC code 81291-7 |
| Observation.component:cytogenomic-nomenclature.value[x] | example | |
| Observation.component:variant-inheritance.code | example | Pattern: variant-inheritance |
| Observation.component:variant-inheritance.value[x] | extensible | VariantInheritance |
| Observation.component:actionability.code | example | Pattern: LOINC code 93348-1 |
| Observation.component:proposed-for-orientation.code | example | Pattern: C0449889 |
| Observation.component:pathogenicity.code | example | Pattern: LOINC code 74019-1 |
| Observation.component:pathogenicity.value[x] | required | Pathogenicity |
| Observation.component:loss-of-heterozygosity.code | example | Pattern: C1881449 |
| Observation.component:segment-intensity.code | example | Pattern: C2732930 |
| Name | Flags | Card. | Type | Description & Constraints | ||||
|---|---|---|---|---|---|---|---|---|
| Observation | C | 0..* | Variant | Variant | ||||
| id | Σ | 0..1 | id | Logical id of this artifact | ||||
| meta | Σ | 0..1 | Meta | Metadata about the resource | ||||
| implicitRules | ?!Σ | 0..1 | uri | A set of rules under which this content was created | ||||
| language | 0..1 | code | Language of the resource content Binding: CommonLanguages (preferred): A human language.
| |||||
| text | 0..1 | Narrative | Text summary of the resource, for human interpretation | |||||
| contained | 0..* | Resource | Contained, inline Resources | |||||
 Slices for extension | 0..* | Extension | Extension Slice: Unordered, Open by value:url | |||||
| BodyStructure | 0..1 | Reference(BodyStructure) | Target anatomic location or structure URL: http://hl7.org/fhir/StructureDefinition/bodySite | |||||
| SecondaryFinding | 0..1 | CodeableConcept | Secondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement.
For more detail, please see:
https://ghr.nlm.nih.gov/primer/testing/secondaryfindings URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding Binding: ObservationCategoryCodes (extensible): Codes to denote a guideline or policy statement.when a genetic test result is being shared as a secondary finding. | |||||
| modifierExtension | ?! | 0..* | Extension | Extensions that cannot be ignored | ||||
| identifier | Σ | 0..* | Identifier | Business Identifier for observation | ||||
| basedOn | Σ | 0..* | Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest) | Fulfills plan, proposal or order | ||||
| partOf | Σ | 0..* | Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy) | Part of referenced event | ||||
| status | ?!Σ | 1..1 | code | registered | preliminary | final | amended + Binding: ObservationStatus (required): Codes providing the status of an observation. | ||||
| category | 1..* | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. Required Pattern: At least the following | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: laboratory | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| code | Σ | 1..1 | CodeableConcept | Genetic variant assessment Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 69548-6 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| subject | Σ | 0..1 | Reference(Oncology Patient) | Who and/or what the observation is about | ||||
| focus | ΣTU | 0..* | Reference(Resource) | What the observation is about, when it is not about the subject of record | ||||
| encounter | Σ | 0..1 | Reference(Encounter) | Healthcare event during which this observation is made | ||||
| Slices for effective[x] | Σ | 0..1 | dateTime | Clinically relevant time/time-period for observation Slice: Unordered, Closed by type:$this | ||||
| effective[x]:effectiveDateTime | Σ | 0..1 | dateTime | Clinically relevant time/time-period for observation | ||||
| issued | Σ | 0..1 | instant | Date/Time this version was made available | ||||
| performer | Σ | 0..1 | Reference(Practitioner | Organization | Patient | RelatedPerson) | Who is responsible for the observation | ||||
| value[x] | ΣC | 1..1 | CodeableConcept | Present|Absent|No call|Indeterminate Binding: LOINC Answer List LL1971-2 (required): Genetic Variant Assessment | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| note | 0..* | Annotation | Comments about the observation | |||||
| bodySite | 0..1 | CodeableConcept | Observed body part Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality. | |||||
| method | 0..1 | CodeableConcept | Sequencing | Oligo aCGH | SNP array | BAC aCGH |Curated|+ Binding: LOINC Answer List LL4048-6 (extensible): Variant analysis method type | |||||
| specimen | 0..1 | Reference(Specimen) | Specimen examined | |||||
| device | 0..1 | Reference(Device | DeviceMetric) | (Measurement) Device | |||||
| referenceRange | C | 0..* | BackboneElement | Provides guide for interpretation | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| low | C | 0..1 | SimpleQuantity | Low Range, if relevant | ||||
| high | C | 0..1 | SimpleQuantity | High Range, if relevant | ||||
| type | 0..1 | CodeableConcept | Reference range qualifier Binding: ObservationReferenceRangeMeaningCodes (preferred): Code for the meaning of a reference range. | |||||
| appliesTo | 0..* | CodeableConcept | Reference range population Binding: ObservationReferenceRangeAppliesToCodes (example): Codes identifying the population the reference range applies to. | |||||
| age | 0..1 | Range | Applicable age range, if relevant | |||||
| text | 0..1 | string | Text based reference range in an observation | |||||
| hasMember | Σ | 0..* | Reference(Observation | QuestionnaireResponse | MolecularSequence) | Related resource that belongs to the Observation group | ||||
| Slices for derivedFrom | Σ | 1..* | Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) | Related measurements the observation is made from Slice: Unordered, Open by pattern:reference | ||||
| derivedFrom:Analysis | Σ | 1..1 | Reference(Sequencing Analysis) | Analysis from which come this observation | ||||
| Slices for component | Σ | 0..* | BackboneElement | Component results Slice: Unordered, Open by pattern:code | ||||
| component:All Slices | Content/Rules for all slices | |||||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. | ||||
 value[x] | Σ | 0..1 | Actual component result | |||||
| valueQuantity | Quantity | |||||||
| valueCodeableConcept | CodeableConcept | |||||||
| valueString | string | |||||||
| valueBoolean | boolean | |||||||
| valueInteger | integer | |||||||
| valueRange | Range | |||||||
| valueRatio | Ratio | |||||||
| valueSampledData | SampledData | |||||||
| valueTime | time | |||||||
| valueDateTime | dateTime | |||||||
| valuePeriod | Period | |||||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:gene-studied | Σ | 0..* | BackboneElement | Gene studied ID | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48018-6 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | CodeableConcept | If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used. Binding: HGNC (extensible): HGNC: Human Gene Nomenclature Committee | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:cytogenetic-location | Σ | 0..* | BackboneElement | Cytogenetic (chromosome) location | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48001-2 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding: (unbound) (example): Binding not yet defined | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:ref-sequence-assembly | Σ | 0..* | BackboneElement | Human reference sequence assembly version | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 62374-4 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding: LOINC Answer List LL1040-6 (extensible): Human reference sequence NCBI build IDs | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:dna-chg | Σ | 0..1 | BackboneElement | DNA Change - Transcript (cHGVS) | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48004-6 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding: HGVS (required): HGVS: Sequence Variant Nomenclature from the Human Genome Variation Society | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:dna-chg-type | Σ | 0..1 | BackboneElement | DNA change type | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48019-4 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | CodeableConcept | Concepts in sequence ontology under SO:0002072 (see http://www.sequenceontology.org/browser/current_release/term/SO:0002072) Binding: DNA Change Type (extensible): DNA Change type values (Sequence Ontology) | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:functional-annotation | Σ | 0..* | BackboneElement | Functional Annotation | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: functional-annotation | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | CodeableConcept | Concepts in sequence ontology under SO:0001537 (see http://www.sequenceontology.org/browser/current_release/term/SO:0001537) Binding: Functional Annotation (extensible): Functional Annotation (Sequence Ontology) | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:variation-code | Σ | 0..1 | BackboneElement | Variation Code | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81252-9 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding: (unbound) (example): Binding not yet defined | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:dbSNP-id | Σ | 0..1 | BackboneElement | dbSNP ID | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81255-2 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding: (unbound) (example): Binding not yet defined | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:genomic-dna-chg | Σ | 0..1 | BackboneElement | DNA Change - Genomic (gHGVS) | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81290-9 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding: HGVS (required): HGVS: Sequence Variant Nomenclature from the Human Genome Variation Society | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:genomic-source-class | Σ | 0..1 | BackboneElement | Genomic source class | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48002-0 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | CodeableConcept | Germline | Somatic | Fetal | Likely germline | Likely somatic |Likely fetal | Unknown genomic origin | De novo Binding: LOINC Answer List LL378-1 (extensible): Genomic source class values | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:amino-acid-chg | Σ | 0..1 | BackboneElement | Amino acid change (pHGVS) | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48005-3 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding: HGVS (required): HGVS: Sequence Variant Nomenclature from the Human Genome Variation Society | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:amino-acid-chg-type | Σ | 0..1 | BackboneElement | Amino acid change type | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48006-1 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | CodeableConcept | Wild type | Deletion | Duplication | Frameshift | Initiating Methionine | Insertion | Insertion and Deletion | Missense | Silent | Stop Codon Mutation Binding: LOINC Answer List LL380-7 (required): Amino acid change type values | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:transcript-ref-seq | Σ | 0..1 | BackboneElement | Transcript reference sequence ID | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 51958-7 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding: (unbound) (example): Binding not yet defined | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:genomic-ref-seq | Σ | 0..1 | BackboneElement | Genomic reference sequence ID | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48013-7 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding: (unbound) (example): Binding not yet defined | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:sample-allelic-frequency | Σ | 0..1 | BackboneElement | Sample Allelic Frequency | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Sample Sample VAF Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81258-6 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | Quantity | Actual component result | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | |||||
| value | Σ | 1..1 | decimal | Numerical value (with implicit precision) | ||||
| comparator | ?!Σ | 0..1 | code | < | <= | >= | > - how to understand the value Binding: QuantityComparator (required): How the Quantity should be understood and represented. | ||||
| unit | Σ | 0..1 | string | Unit representation | ||||
| system | ΣC | 1..1 | uri | System that defines coded unit form Fixed Value: http://unitsofmeasure.org | ||||
| code | Σ | 0..1 | code | Coded form of the unit | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:allelic-read-depth | Σ | 0..* | BackboneElement | Allelic read depth | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 82121-5 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | Quantity | Actual component result | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:allelic-state | Σ | 0..1 | BackboneElement | Allelic state | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 53034-5 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | CodeableConcept | Heteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous Binding: LOINC Answer List LL381-5 (extensible): Allelic state type values | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:copy-number | Σ | 0..1 | BackboneElement | Genomic structural variant copy number | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 82155-3 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | C | 1..1 | Count | A measured or measurable amount | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:ref-allele | Σ | 0..1 | BackboneElement | Genomic ref allele | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 69547-8 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | string | Actual component result | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:alt-allele | Σ | 0..1 | BackboneElement | Genomic alt allele | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 69551-0 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | string | Actual component result | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:coordinate-system | Σ | 0..1 | BackboneElement | Coordinate System | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 92822-6 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | CodeableConcept | 0-based interval | 0-based character | 1-based character Binding: LOINC Answer List LL5323-2 (preferred): Base coordinate systems start and end measurements for variants | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:exact-start-end | Σ | 0..1 | BackboneElement | Exact start-end | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: exact-start-end | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | Range | Actual component result | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | |||||
| low | Σ | 1..1 | SimpleQuantity | Exact Start | ||||
| high | Σ | 0..1 | SimpleQuantity | Exact End | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:variant-length | Σ | 0..1 | BackboneElement | Structural variant length | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81300-6 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | C | 1..1 | Count | A measured or measurable amount | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:outer-start-end | Σ | 0..1 | BackboneElement | Variant outer start and end | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: outer-start-end | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | Range | Actual component result | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | |||||
| low | Σ | 1..1 | SimpleQuantity | Low limit | ||||
| high | Σ | 1..1 | SimpleQuantity | High limit | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:inner-start-end | Σ | 0..1 | BackboneElement | Variant inner start and end | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: inner-start-end | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | Range | Actual component result | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | |||||
| low | Σ | 1..1 | SimpleQuantity | Low limit | ||||
| high | Σ | 1..1 | SimpleQuantity | High limit | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:chromosome-copy-number-change-type | Σ | 0..1 | BackboneElement | Chromosome copy number change type | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 62378-5 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | CodeableConcept | Copy number gain | Copy number loss Binding: LOINC Answer List LL1041-4 (required): Copy Number Change Types | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:arrCGH-ratio | Σ | 0..1 | BackboneElement | Structural variant reported arrCGH [Ratio] | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81299-0 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | C | 1..1 | SimpleQuantity | A fixed quantity (no comparator) | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:complex-var-type | Σ | 0..1 | BackboneElement | Complex variant type | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81263-6 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | CodeableConcept | Compound heterozygous | Double heterozygous | Haplotype | Hemizygous Binding: LOINC Answer List LL3999-1 (required): Complex variant type | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:cytogenomic-nomenclature | Σ | 0..1 | BackboneElement | Cytogenomic Nomenclature | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Variant ISCN Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81291-7 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding: (unbound) (example): Binding not yet defined | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:variant-inheritance | Σ | 0..1 | BackboneElement | Variant Inheritance | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: variant-inheritance | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding: Variant Inheritance (extensible): Variant Inheritance (Sequence Ontology) | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:actionability | Σ | 0..1 | BackboneElement | Conclusion of the clinicians wether the variant is actionable or not during the Molecular Tumor Board | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 93348-1 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| Slices for value[x] | Σ | 0..1 | boolean | Actual component result Slice: Unordered, Closed by type:$this | ||||
| value[x]:valueBoolean | Σ | 0..1 | boolean | Actual component result | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:proposed-for-orientation | Σ | 0..1 | BackboneElement | Is the ClinicalTumorBoardConclusion used to orient the treatment decision ? | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/umls | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: C0449889 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| Slices for value[x] | Σ | 0..1 | boolean | Actual component result Slice: Unordered, Closed by type:$this | ||||
| value[x]:valueBoolean | Σ | 0..1 | boolean | Actual component result | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:pathogenicity | Σ | 0..1 | BackboneElement | Conclusion of the biologist on the pathogenicity of the variant before the Molecular Tumor Board | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 74019-1 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| Slices for value[x] | Σ | 0..1 | CodeableConcept | Actual component result Slice: Unordered, Closed by type:$this Binding: Pathogenicity Value Set (required) | ||||
| value[x]:valueCodeableConcept | Σ | 0..1 | CodeableConcept | Actual component result | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:loss-of-heterozygosity | Σ | 0..1 | BackboneElement | Is the segment located in a region of loss of heterozygosity ? (can be independant from copy number information | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/umls | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: C1881449 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| Slices for value[x] | Σ | 0..1 | boolean | Actual component result Slice: Unordered, Closed by type:$this | ||||
| value[x]:valueBoolean | Σ | 0..1 | boolean | Actual component result | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:segment-intensity | Σ | 0..1 | BackboneElement | Intensity of the measured signal | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/umls | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: C2732930 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| Slices for value[x] | Σ | 0..1 | integer | Actual component result Slice: Unordered, Closed by type:$this | ||||
| value[x]:valueInteger | Σ | 0..1 | integer | Actual component result | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| Documentation for this format | ||||||||
| Path | Conformance | ValueSet / Code | ||||
| Observation.language | preferred | CommonLanguages
| ||||
| Observation.status | required | ObservationStatus | ||||
| Observation.category | preferred | Pattern: laboratory | ||||
| Observation.code | example | Pattern: LOINC code 69548-6 | ||||
| Observation.value[x] | required | LOINC LL1971-2 | ||||
| Observation.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.bodySite | example | SNOMEDCTBodyStructures | ||||
| Observation.method | extensible | LOINC LL4048-6 | ||||
| Observation.referenceRange.type | preferred | ObservationReferenceRangeMeaningCodes | ||||
| Observation.referenceRange.appliesTo | example | ObservationReferenceRangeAppliesToCodes | ||||
| Observation.component.code | example | LOINCCodes (a valid code from LOINC) | ||||
| Observation.component.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:gene-studied.code | example | Pattern: LOINC code 48018-6 | ||||
| Observation.component:gene-studied.value[x] | extensible | HGNC | ||||
| Observation.component:gene-studied.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:cytogenetic-location.code | example | Pattern: LOINC code 48001-2 | ||||
| Observation.component:cytogenetic-location.value[x] | example | |||||
| Observation.component:cytogenetic-location.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:ref-sequence-assembly.code | example | Pattern: LOINC code 62374-4 | ||||
| Observation.component:ref-sequence-assembly.value[x] | extensible | LOINC LL1040-6 | ||||
| Observation.component:ref-sequence-assembly.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:dna-chg.code | example | Pattern: LOINC code 48004-6 | ||||
| Observation.component:dna-chg.value[x] | required | HGVS | ||||
| Observation.component:dna-chg.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:dna-chg-type.code | example | Pattern: LOINC code 48019-4 | ||||
| Observation.component:dna-chg-type.value[x] | extensible | DnaChangeType | ||||
| Observation.component:dna-chg-type.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:functional-annotation.code | example | Pattern: functional-annotation | ||||
| Observation.component:functional-annotation.value[x] | extensible | FunctionalAnnotation | ||||
| Observation.component:functional-annotation.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:variation-code.code | example | Pattern: LOINC code 81252-9 | ||||
| Observation.component:variation-code.value[x] | example | |||||
| Observation.component:variation-code.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:dbSNP-id.code | example | Pattern: LOINC code 81255-2 | ||||
| Observation.component:dbSNP-id.value[x] | example | |||||
| Observation.component:dbSNP-id.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:genomic-dna-chg.code | example | Pattern: LOINC code 81290-9 | ||||
| Observation.component:genomic-dna-chg.value[x] | required | HGVS | ||||
| Observation.component:genomic-dna-chg.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:genomic-source-class.code | example | Pattern: LOINC code 48002-0 | ||||
| Observation.component:genomic-source-class.value[x] | extensible | LOINC LL378-1 | ||||
| Observation.component:genomic-source-class.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:amino-acid-chg.code | example | Pattern: LOINC code 48005-3 | ||||
| Observation.component:amino-acid-chg.value[x] | required | HGVS | ||||
| Observation.component:amino-acid-chg.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:amino-acid-chg-type.code | example | Pattern: LOINC code 48006-1 | ||||
| Observation.component:amino-acid-chg-type.value[x] | required | LOINC LL380-7 | ||||
| Observation.component:amino-acid-chg-type.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:transcript-ref-seq.code | example | Pattern: LOINC code 51958-7 | ||||
| Observation.component:transcript-ref-seq.value[x] | example | |||||
| Observation.component:transcript-ref-seq.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:genomic-ref-seq.code | example | Pattern: LOINC code 48013-7 | ||||
| Observation.component:genomic-ref-seq.value[x] | example | |||||
| Observation.component:genomic-ref-seq.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:sample-allelic-frequency.code | example | Pattern: LOINC code 81258-6 | ||||
| Observation.component:sample-allelic-frequency.value[x].comparator | required | QuantityComparator | ||||
| Observation.component:sample-allelic-frequency.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:allelic-read-depth.code | example | Pattern: LOINC code 82121-5 | ||||
| Observation.component:allelic-read-depth.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:allelic-state.code | example | Pattern: LOINC code 53034-5 | ||||
| Observation.component:allelic-state.value[x] | extensible | LOINC LL381-5 | ||||
| Observation.component:allelic-state.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:copy-number.code | example | Pattern: LOINC code 82155-3 | ||||
| Observation.component:copy-number.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:ref-allele.code | example | Pattern: LOINC code 69547-8 | ||||
| Observation.component:ref-allele.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:alt-allele.code | example | Pattern: LOINC code 69551-0 | ||||
| Observation.component:alt-allele.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:coordinate-system.code | example | Pattern: LOINC code 92822-6 | ||||
| Observation.component:coordinate-system.value[x] | preferred | LOINC LL5323-2 | ||||
| Observation.component:coordinate-system.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:exact-start-end.code | example | Pattern: exact-start-end | ||||
| Observation.component:exact-start-end.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:variant-length.code | example | Pattern: LOINC code 81300-6 | ||||
| Observation.component:variant-length.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:outer-start-end.code | example | Pattern: outer-start-end | ||||
| Observation.component:outer-start-end.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:inner-start-end.code | example | Pattern: inner-start-end | ||||
| Observation.component:inner-start-end.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:chromosome-copy-number-change-type.code | example | Pattern: LOINC code 62378-5 | ||||
| Observation.component:chromosome-copy-number-change-type.value[x] | required | LOINC LL1041-4 | ||||
| Observation.component:chromosome-copy-number-change-type.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:arrCGH-ratio.code | example | Pattern: LOINC code 81299-0 | ||||
| Observation.component:arrCGH-ratio.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:complex-var-type.code | example | Pattern: LOINC code 81263-6 | ||||
| Observation.component:complex-var-type.value[x] | required | LOINC LL3999-1 | ||||
| Observation.component:complex-var-type.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:cytogenomic-nomenclature.code | example | Pattern: LOINC code 81291-7 | ||||
| Observation.component:cytogenomic-nomenclature.value[x] | example | |||||
| Observation.component:cytogenomic-nomenclature.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:variant-inheritance.code | example | Pattern: variant-inheritance | ||||
| Observation.component:variant-inheritance.value[x] | extensible | VariantInheritance | ||||
| Observation.component:variant-inheritance.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:actionability.code | example | Pattern: LOINC code 93348-1 | ||||
| Observation.component:actionability.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:proposed-for-orientation.code | example | Pattern: C0449889 | ||||
| Observation.component:proposed-for-orientation.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:pathogenicity.code | example | Pattern: LOINC code 74019-1 | ||||
| Observation.component:pathogenicity.value[x] | required | Pathogenicity | ||||
| Observation.component:pathogenicity.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:loss-of-heterozygosity.code | example | Pattern: C1881449 | ||||
| Observation.component:loss-of-heterozygosity.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:segment-intensity.code | example | Pattern: C2732930 | ||||
| Observation.component:segment-intensity.dataAbsentReason | extensible | DataAbsentReason |
This structure is derived from Variant
Summary
Mandatory: 2 elements (4 nested mandatory elements)
Structures
This structure refers to these other structures:
Slices
This structure defines the following Slices:
Differential View
This structure is derived from Variant
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
| Observation | 0..* | Variant | Variant | |
| subject | 0..1 | Reference(Oncology Patient) | Who and/or what the observation is about | |
| Slices for derivedFrom | 1..* | Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) | Related measurements the observation is made from Slice: Unordered, Open by pattern:reference | |
| derivedFrom:Analysis | 1..1 | Reference(Sequencing Analysis) | Analysis from which come this observation | |
| component:cytogenetic-location | 0..* | BackboneElement | Cytogenetic (chromosome) location | |
| component:ref-sequence-assembly | 0..* | BackboneElement | Human reference sequence assembly version | |
| valueCodeableConcept | 1..1 | CodeableConcept | Actual component result | |
| component:variation-code | 0..1 | BackboneElement | Variation Code | |
| valueCodeableConcept | 1..1 | CodeableConcept | Actual component result | |
| component:copy-number | 0..1 | BackboneElement | Genomic structural variant copy number | |
| valueQuantity | 1..1 | Count | A measured or measurable amount | |
| component:exact-start-end | 0..1 | BackboneElement | Exact start-end | |
| valueRange | 1..1 | Range | Actual component result | |
| low | 1..1 | SimpleQuantity | Exact Start | |
| high | 0..1 | SimpleQuantity | Exact End | |
| component:variant-length | 0..1 | BackboneElement | Structural variant length | |
| component:actionability | 0..1 | BackboneElement | Conclusion of the clinicians wether the variant is actionable or not during the Molecular Tumor Board | |
| code | 1..1 | CodeableConcept | Type of component observation (code / type) Required Pattern: At least the following | |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 93348-1 | |
| value[x] | 0..1 | boolean | Actual component result Slice: Unordered, Open by type:$this | |
| valueBoolean | 0..1 | boolean | Actual component result | |
| component:proposed-for-orientation | 0..1 | BackboneElement | Is the ClinicalTumorBoardConclusion used to orient the treatment decision ? | |
| code | 1..1 | CodeableConcept | Type of component observation (code / type) Required Pattern: At least the following | |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/umls | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: C0449889 | |
| value[x] | 0..1 | boolean | Actual component result Slice: Unordered, Open by type:$this | |
| valueBoolean | 0..1 | boolean | Actual component result | |
| component:pathogenicity | 0..1 | BackboneElement | Conclusion of the biologist on the pathogenicity of the variant before the Molecular Tumor Board | |
| code | 1..1 | CodeableConcept | Type of component observation (code / type) Required Pattern: At least the following | |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 74019-1 | |
| value[x] | 0..1 | CodeableConcept | Actual component result Slice: Unordered, Open by type:$this Binding: Pathogenicity Value Set (required) | |
| valueCodeableConcept | 0..1 | CodeableConcept | Actual component result | |
| component:loss-of-heterozygosity | 0..1 | BackboneElement | Is the segment located in a region of loss of heterozygosity ? (can be independant from copy number information | |
| code | 1..1 | CodeableConcept | Type of component observation (code / type) Required Pattern: At least the following | |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/umls | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: C1881449 | |
| value[x] | 0..1 | boolean | Actual component result Slice: Unordered, Open by type:$this | |
| valueBoolean | 0..1 | boolean | Actual component result | |
| component:segment-intensity | 0..1 | BackboneElement | Intensity of the measured signal | |
| code | 1..1 | CodeableConcept | Type of component observation (code / type) Required Pattern: At least the following | |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/umls | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: C2732930 | |
| value[x] | 0..1 | integer | Actual component result Slice: Unordered, Open by type:$this | |
| valueInteger | 0..1 | integer | Actual component result | |
| Documentation for this format | ||||
| Path | Conformance | ValueSet |
| Observation.component:pathogenicity.value[x] | required | Pathogenicity |
Key Elements View
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
| Observation | C | 0..* | Variant | Variant |
| implicitRules | ?!Σ | 0..1 | uri | A set of rules under which this content was created |
| BodyStructure | 0..1 | Reference(BodyStructure) | Target anatomic location or structure URL: http://hl7.org/fhir/StructureDefinition/bodySite | |
| SecondaryFinding | 0..1 | CodeableConcept | Secondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement.
For more detail, please see:
https://ghr.nlm.nih.gov/primer/testing/secondaryfindings URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding Binding: ObservationCategoryCodes (extensible): Codes to denote a guideline or policy statement.when a genetic test result is being shared as a secondary finding. | |
| modifierExtension | ?! | 0..* | Extension | Extensions that cannot be ignored |
| status | ?!Σ | 1..1 | code | registered | preliminary | final | amended + Binding: ObservationStatus (required): Codes providing the status of an observation. |
| category | 1..* | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. Required Pattern: At least the following | |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: laboratory | |
| code | Σ | 1..1 | CodeableConcept | Genetic variant assessment Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 69548-6 | |
| subject | Σ | 0..1 | Reference(Oncology Patient) | Who and/or what the observation is about |
| Slices for effective[x] | Σ | 0..1 | dateTime | Clinically relevant time/time-period for observation Slice: Unordered, Closed by type:$this |
| effective[x]:effectiveDateTime | Σ | 0..1 | dateTime | Clinically relevant time/time-period for observation |
| performer | Σ | 0..1 | Reference(Practitioner | Organization | Patient | RelatedPerson) | Who is responsible for the observation |
| value[x] | ΣC | 1..1 | CodeableConcept | Present|Absent|No call|Indeterminate Binding: LOINC Answer List LL1971-2 (required): Genetic Variant Assessment |
| Slices for derivedFrom | Σ | 1..* | Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) | Related measurements the observation is made from Slice: Unordered, Open by pattern:reference |
| derivedFrom:Analysis | Σ | 1..1 | Reference(Sequencing Analysis) | Analysis from which come this observation |
| Slices for component | Σ | 0..* | BackboneElement | Component results Slice: Unordered, Open by pattern:code |
| component:All Slices | Content/Rules for all slices | |||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. |
| component:gene-studied | Σ | 0..* | BackboneElement | Gene studied ID |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48018-6 | |
| value[x] | Σ | 1..1 | CodeableConcept | If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used. Binding: HGNC (extensible): HGNC: Human Gene Nomenclature Committee |
| component:cytogenetic-location | Σ | 0..* | BackboneElement | Cytogenetic (chromosome) location |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48001-2 | |
| value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding: (unbound) (example): Binding not yet defined |
| component:ref-sequence-assembly | Σ | 0..* | BackboneElement | Human reference sequence assembly version |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 62374-4 | |
| value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding: LOINC Answer List LL1040-6 (extensible): Human reference sequence NCBI build IDs |
| component:dna-chg | Σ | 0..1 | BackboneElement | DNA Change - Transcript (cHGVS) |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48004-6 | |
| value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding: HGVS (required): HGVS: Sequence Variant Nomenclature from the Human Genome Variation Society |
| component:dna-chg-type | Σ | 0..1 | BackboneElement | DNA change type |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48019-4 | |
| value[x] | Σ | 1..1 | CodeableConcept | Concepts in sequence ontology under SO:0002072 (see http://www.sequenceontology.org/browser/current_release/term/SO:0002072) Binding: DNA Change Type (extensible): DNA Change type values (Sequence Ontology) |
| component:functional-annotation | Σ | 0..* | BackboneElement | Functional Annotation |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: functional-annotation | |
| value[x] | Σ | 1..1 | CodeableConcept | Concepts in sequence ontology under SO:0001537 (see http://www.sequenceontology.org/browser/current_release/term/SO:0001537) Binding: Functional Annotation (extensible): Functional Annotation (Sequence Ontology) |
| component:variation-code | Σ | 0..1 | BackboneElement | Variation Code |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81252-9 | |
| value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding: (unbound) (example): Binding not yet defined |
| component:dbSNP-id | Σ | 0..1 | BackboneElement | dbSNP ID |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81255-2 | |
| value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding: (unbound) (example): Binding not yet defined |
| component:genomic-dna-chg | Σ | 0..1 | BackboneElement | DNA Change - Genomic (gHGVS) |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81290-9 | |
| value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding: HGVS (required): HGVS: Sequence Variant Nomenclature from the Human Genome Variation Society |
| component:genomic-source-class | Σ | 0..1 | BackboneElement | Genomic source class |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48002-0 | |
| value[x] | Σ | 1..1 | CodeableConcept | Germline | Somatic | Fetal | Likely germline | Likely somatic |Likely fetal | Unknown genomic origin | De novo Binding: LOINC Answer List LL378-1 (extensible): Genomic source class values |
| component:amino-acid-chg | Σ | 0..1 | BackboneElement | Amino acid change (pHGVS) |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48005-3 | |
| value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding: HGVS (required): HGVS: Sequence Variant Nomenclature from the Human Genome Variation Society |
| component:amino-acid-chg-type | Σ | 0..1 | BackboneElement | Amino acid change type |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48006-1 | |
| value[x] | Σ | 1..1 | CodeableConcept | Wild type | Deletion | Duplication | Frameshift | Initiating Methionine | Insertion | Insertion and Deletion | Missense | Silent | Stop Codon Mutation Binding: LOINC Answer List LL380-7 (required): Amino acid change type values |
| component:transcript-ref-seq | Σ | 0..1 | BackboneElement | Transcript reference sequence ID |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 51958-7 | |
| value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding: (unbound) (example): Binding not yet defined |
| component:genomic-ref-seq | Σ | 0..1 | BackboneElement | Genomic reference sequence ID |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48013-7 | |
| value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding: (unbound) (example): Binding not yet defined |
| component:sample-allelic-frequency | Σ | 0..1 | BackboneElement | Sample Allelic Frequency |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Sample Sample VAF Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81258-6 | |
| value[x] | Σ | 1..1 | Quantity | Actual component result |
| value | Σ | 1..1 | decimal | Numerical value (with implicit precision) |
| comparator | ?!Σ | 0..1 | code | < | <= | >= | > - how to understand the value Binding: QuantityComparator (required): How the Quantity should be understood and represented. |
| system | ΣC | 1..1 | uri | System that defines coded unit form Fixed Value: http://unitsofmeasure.org |
| component:allelic-read-depth | Σ | 0..* | BackboneElement | Allelic read depth |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 82121-5 | |
| value[x] | Σ | 1..1 | Quantity | Actual component result |
| component:allelic-state | Σ | 0..1 | BackboneElement | Allelic state |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 53034-5 | |
| value[x] | Σ | 1..1 | CodeableConcept | Heteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous Binding: LOINC Answer List LL381-5 (extensible): Allelic state type values |
| component:copy-number | Σ | 0..1 | BackboneElement | Genomic structural variant copy number |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 82155-3 | |
| value[x] | C | 1..1 | Count | A measured or measurable amount |
| component:ref-allele | Σ | 0..1 | BackboneElement | Genomic ref allele |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 69547-8 | |
| value[x] | Σ | 1..1 | string | Actual component result |
| component:alt-allele | Σ | 0..1 | BackboneElement | Genomic alt allele |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 69551-0 | |
| value[x] | Σ | 1..1 | string | Actual component result |
| component:coordinate-system | Σ | 0..1 | BackboneElement | Coordinate System |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 92822-6 | |
| value[x] | Σ | 1..1 | CodeableConcept | 0-based interval | 0-based character | 1-based character Binding: LOINC Answer List LL5323-2 (preferred): Base coordinate systems start and end measurements for variants |
| component:exact-start-end | Σ | 0..1 | BackboneElement | Exact start-end |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: exact-start-end | |
| value[x] | Σ | 1..1 | Range | Actual component result |
| low | Σ | 1..1 | SimpleQuantity | Exact Start |
| component:variant-length | Σ | 0..1 | BackboneElement | Structural variant length |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81300-6 | |
| value[x] | C | 1..1 | Count | A measured or measurable amount |
| component:outer-start-end | Σ | 0..1 | BackboneElement | Variant outer start and end |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: outer-start-end | |
| value[x] | Σ | 1..1 | Range | Actual component result |
| low | Σ | 1..1 | SimpleQuantity | Low limit |
| high | Σ | 1..1 | SimpleQuantity | High limit |
| component:inner-start-end | Σ | 0..1 | BackboneElement | Variant inner start and end |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: inner-start-end | |
| value[x] | Σ | 1..1 | Range | Actual component result |
| low | Σ | 1..1 | SimpleQuantity | Low limit |
| high | Σ | 1..1 | SimpleQuantity | High limit |
| component:chromosome-copy-number-change-type | Σ | 0..1 | BackboneElement | Chromosome copy number change type |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 62378-5 | |
| value[x] | Σ | 1..1 | CodeableConcept | Copy number gain | Copy number loss Binding: LOINC Answer List LL1041-4 (required): Copy Number Change Types |
| component:arrCGH-ratio | Σ | 0..1 | BackboneElement | Structural variant reported arrCGH [Ratio] |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81299-0 | |
| value[x] | C | 1..1 | SimpleQuantity | A fixed quantity (no comparator) |
| component:complex-var-type | Σ | 0..1 | BackboneElement | Complex variant type |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81263-6 | |
| value[x] | Σ | 1..1 | CodeableConcept | Compound heterozygous | Double heterozygous | Haplotype | Hemizygous Binding: LOINC Answer List LL3999-1 (required): Complex variant type |
| component:cytogenomic-nomenclature | Σ | 0..1 | BackboneElement | Cytogenomic Nomenclature |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Variant ISCN Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81291-7 | |
| value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding: (unbound) (example): Binding not yet defined |
| component:variant-inheritance | Σ | 0..1 | BackboneElement | Variant Inheritance |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: variant-inheritance | |
| value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding: Variant Inheritance (extensible): Variant Inheritance (Sequence Ontology) |
| component:actionability | Σ | 0..1 | BackboneElement | Conclusion of the clinicians wether the variant is actionable or not during the Molecular Tumor Board |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 93348-1 | |
| Slices for value[x] | Σ | 0..1 | boolean | Actual component result Slice: Unordered, Closed by type:$this |
| value[x]:valueBoolean | Σ | 0..1 | boolean | Actual component result |
| component:proposed-for-orientation | Σ | 0..1 | BackboneElement | Is the ClinicalTumorBoardConclusion used to orient the treatment decision ? |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/umls | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: C0449889 | |
| Slices for value[x] | Σ | 0..1 | boolean | Actual component result Slice: Unordered, Closed by type:$this |
| value[x]:valueBoolean | Σ | 0..1 | boolean | Actual component result |
| component:pathogenicity | Σ | 0..1 | BackboneElement | Conclusion of the biologist on the pathogenicity of the variant before the Molecular Tumor Board |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 74019-1 | |
| Slices for value[x] | Σ | 0..1 | CodeableConcept | Actual component result Slice: Unordered, Closed by type:$this Binding: Pathogenicity Value Set (required) |
| value[x]:valueCodeableConcept | Σ | 0..1 | CodeableConcept | Actual component result |
| component:loss-of-heterozygosity | Σ | 0..1 | BackboneElement | Is the segment located in a region of loss of heterozygosity ? (can be independant from copy number information |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/umls | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: C1881449 | |
| Slices for value[x] | Σ | 0..1 | boolean | Actual component result Slice: Unordered, Closed by type:$this |
| value[x]:valueBoolean | Σ | 0..1 | boolean | Actual component result |
| component:segment-intensity | Σ | 0..1 | BackboneElement | Intensity of the measured signal |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/umls | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: C2732930 | |
| Slices for value[x] | Σ | 0..1 | integer | Actual component result Slice: Unordered, Closed by type:$this |
| value[x]:valueInteger | Σ | 0..1 | integer | Actual component result |
| Documentation for this format | ||||
| Path | Conformance | ValueSet / Code |
| Observation.status | required | ObservationStatus |
| Observation.category | preferred | Pattern: laboratory |
| Observation.code | example | Pattern: LOINC code 69548-6 |
| Observation.value[x] | required | LOINC LL1971-2 |
| Observation.component.code | example | LOINCCodes (a valid code from LOINC) |
| Observation.component:gene-studied.code | example | Pattern: LOINC code 48018-6 |
| Observation.component:gene-studied.value[x] | extensible | HGNC |
| Observation.component:cytogenetic-location.code | example | Pattern: LOINC code 48001-2 |
| Observation.component:cytogenetic-location.value[x] | example | |
| Observation.component:ref-sequence-assembly.code | example | Pattern: LOINC code 62374-4 |
| Observation.component:ref-sequence-assembly.value[x] | extensible | LOINC LL1040-6 |
| Observation.component:dna-chg.code | example | Pattern: LOINC code 48004-6 |
| Observation.component:dna-chg.value[x] | required | HGVS |
| Observation.component:dna-chg-type.code | example | Pattern: LOINC code 48019-4 |
| Observation.component:dna-chg-type.value[x] | extensible | DnaChangeType |
| Observation.component:functional-annotation.code | example | Pattern: functional-annotation |
| Observation.component:functional-annotation.value[x] | extensible | FunctionalAnnotation |
| Observation.component:variation-code.code | example | Pattern: LOINC code 81252-9 |
| Observation.component:variation-code.value[x] | example | |
| Observation.component:dbSNP-id.code | example | Pattern: LOINC code 81255-2 |
| Observation.component:dbSNP-id.value[x] | example | |
| Observation.component:genomic-dna-chg.code | example | Pattern: LOINC code 81290-9 |
| Observation.component:genomic-dna-chg.value[x] | required | HGVS |
| Observation.component:genomic-source-class.code | example | Pattern: LOINC code 48002-0 |
| Observation.component:genomic-source-class.value[x] | extensible | LOINC LL378-1 |
| Observation.component:amino-acid-chg.code | example | Pattern: LOINC code 48005-3 |
| Observation.component:amino-acid-chg.value[x] | required | HGVS |
| Observation.component:amino-acid-chg-type.code | example | Pattern: LOINC code 48006-1 |
| Observation.component:amino-acid-chg-type.value[x] | required | LOINC LL380-7 |
| Observation.component:transcript-ref-seq.code | example | Pattern: LOINC code 51958-7 |
| Observation.component:transcript-ref-seq.value[x] | example | |
| Observation.component:genomic-ref-seq.code | example | Pattern: LOINC code 48013-7 |
| Observation.component:genomic-ref-seq.value[x] | example | |
| Observation.component:sample-allelic-frequency.code | example | Pattern: LOINC code 81258-6 |
| Observation.component:sample-allelic-frequency.value[x].comparator | required | QuantityComparator |
| Observation.component:allelic-read-depth.code | example | Pattern: LOINC code 82121-5 |
| Observation.component:allelic-state.code | example | Pattern: LOINC code 53034-5 |
| Observation.component:allelic-state.value[x] | extensible | LOINC LL381-5 |
| Observation.component:copy-number.code | example | Pattern: LOINC code 82155-3 |
| Observation.component:ref-allele.code | example | Pattern: LOINC code 69547-8 |
| Observation.component:alt-allele.code | example | Pattern: LOINC code 69551-0 |
| Observation.component:coordinate-system.code | example | Pattern: LOINC code 92822-6 |
| Observation.component:coordinate-system.value[x] | preferred | LOINC LL5323-2 |
| Observation.component:exact-start-end.code | example | Pattern: exact-start-end |
| Observation.component:variant-length.code | example | Pattern: LOINC code 81300-6 |
| Observation.component:outer-start-end.code | example | Pattern: outer-start-end |
| Observation.component:inner-start-end.code | example | Pattern: inner-start-end |
| Observation.component:chromosome-copy-number-change-type.code | example | Pattern: LOINC code 62378-5 |
| Observation.component:chromosome-copy-number-change-type.value[x] | required | LOINC LL1041-4 |
| Observation.component:arrCGH-ratio.code | example | Pattern: LOINC code 81299-0 |
| Observation.component:complex-var-type.code | example | Pattern: LOINC code 81263-6 |
| Observation.component:complex-var-type.value[x] | required | LOINC LL3999-1 |
| Observation.component:cytogenomic-nomenclature.code | example | Pattern: LOINC code 81291-7 |
| Observation.component:cytogenomic-nomenclature.value[x] | example | |
| Observation.component:variant-inheritance.code | example | Pattern: variant-inheritance |
| Observation.component:variant-inheritance.value[x] | extensible | VariantInheritance |
| Observation.component:actionability.code | example | Pattern: LOINC code 93348-1 |
| Observation.component:proposed-for-orientation.code | example | Pattern: C0449889 |
| Observation.component:pathogenicity.code | example | Pattern: LOINC code 74019-1 |
| Observation.component:pathogenicity.value[x] | required | Pathogenicity |
| Observation.component:loss-of-heterozygosity.code | example | Pattern: C1881449 |
| Observation.component:segment-intensity.code | example | Pattern: C2732930 |
Snapshot View
| Name | Flags | Card. | Type | Description & Constraints | ||||
|---|---|---|---|---|---|---|---|---|
| Observation | C | 0..* | Variant | Variant | ||||
| id | Σ | 0..1 | id | Logical id of this artifact | ||||
| meta | Σ | 0..1 | Meta | Metadata about the resource | ||||
| implicitRules | ?!Σ | 0..1 | uri | A set of rules under which this content was created | ||||
| language | 0..1 | code | Language of the resource content Binding: CommonLanguages (preferred): A human language.
| |||||
| text | 0..1 | Narrative | Text summary of the resource, for human interpretation | |||||
| contained | 0..* | Resource | Contained, inline Resources | |||||
| Slices for extension | 0..* | Extension | Extension Slice: Unordered, Open by value:url | |||||
| BodyStructure | 0..1 | Reference(BodyStructure) | Target anatomic location or structure URL: http://hl7.org/fhir/StructureDefinition/bodySite | |||||
| SecondaryFinding | 0..1 | CodeableConcept | Secondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement.
For more detail, please see:
https://ghr.nlm.nih.gov/primer/testing/secondaryfindings URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding Binding: ObservationCategoryCodes (extensible): Codes to denote a guideline or policy statement.when a genetic test result is being shared as a secondary finding. | |||||
| modifierExtension | ?! | 0..* | Extension | Extensions that cannot be ignored | ||||
| identifier | Σ | 0..* | Identifier | Business Identifier for observation | ||||
| basedOn | Σ | 0..* | Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest) | Fulfills plan, proposal or order | ||||
| partOf | Σ | 0..* | Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy) | Part of referenced event | ||||
| status | ?!Σ | 1..1 | code | registered | preliminary | final | amended + Binding: ObservationStatus (required): Codes providing the status of an observation. | ||||
| category | 1..* | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. Required Pattern: At least the following | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: laboratory | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| code | Σ | 1..1 | CodeableConcept | Genetic variant assessment Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 69548-6 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| subject | Σ | 0..1 | Reference(Oncology Patient) | Who and/or what the observation is about | ||||
| focus | ΣTU | 0..* | Reference(Resource) | What the observation is about, when it is not about the subject of record | ||||
| encounter | Σ | 0..1 | Reference(Encounter) | Healthcare event during which this observation is made | ||||
| Slices for effective[x] | Σ | 0..1 | dateTime | Clinically relevant time/time-period for observation Slice: Unordered, Closed by type:$this | ||||
| effective[x]:effectiveDateTime | Σ | 0..1 | dateTime | Clinically relevant time/time-period for observation | ||||
| issued | Σ | 0..1 | instant | Date/Time this version was made available | ||||
| performer | Σ | 0..1 | Reference(Practitioner | Organization | Patient | RelatedPerson) | Who is responsible for the observation | ||||
| value[x] | ΣC | 1..1 | CodeableConcept | Present|Absent|No call|Indeterminate Binding: LOINC Answer List LL1971-2 (required): Genetic Variant Assessment | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| note | 0..* | Annotation | Comments about the observation | |||||
| bodySite | 0..1 | CodeableConcept | Observed body part Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality. | |||||
| method | 0..1 | CodeableConcept | Sequencing | Oligo aCGH | SNP array | BAC aCGH |Curated|+ Binding: LOINC Answer List LL4048-6 (extensible): Variant analysis method type | |||||
| specimen | 0..1 | Reference(Specimen) | Specimen examined | |||||
| device | 0..1 | Reference(Device | DeviceMetric) | (Measurement) Device | |||||
| referenceRange | C | 0..* | BackboneElement | Provides guide for interpretation | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| low | C | 0..1 | SimpleQuantity | Low Range, if relevant | ||||
| high | C | 0..1 | SimpleQuantity | High Range, if relevant | ||||
| type | 0..1 | CodeableConcept | Reference range qualifier Binding: ObservationReferenceRangeMeaningCodes (preferred): Code for the meaning of a reference range. | |||||
| appliesTo | 0..* | CodeableConcept | Reference range population Binding: ObservationReferenceRangeAppliesToCodes (example): Codes identifying the population the reference range applies to. | |||||
| age | 0..1 | Range | Applicable age range, if relevant | |||||
| text | 0..1 | string | Text based reference range in an observation | |||||
| hasMember | Σ | 0..* | Reference(Observation | QuestionnaireResponse | MolecularSequence) | Related resource that belongs to the Observation group | ||||
| Slices for derivedFrom | Σ | 1..* | Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) | Related measurements the observation is made from Slice: Unordered, Open by pattern:reference | ||||
| derivedFrom:Analysis | Σ | 1..1 | Reference(Sequencing Analysis) | Analysis from which come this observation | ||||
| Slices for component | Σ | 0..* | BackboneElement | Component results Slice: Unordered, Open by pattern:code | ||||
| component:All Slices | Content/Rules for all slices | |||||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. | ||||
| value[x] | Σ | 0..1 | Actual component result | |||||
| valueQuantity | Quantity | |||||||
| valueCodeableConcept | CodeableConcept | |||||||
| valueString | string | |||||||
| valueBoolean | boolean | |||||||
| valueInteger | integer | |||||||
| valueRange | Range | |||||||
| valueRatio | Ratio | |||||||
| valueSampledData | SampledData | |||||||
| valueTime | time | |||||||
| valueDateTime | dateTime | |||||||
| valuePeriod | Period | |||||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:gene-studied | Σ | 0..* | BackboneElement | Gene studied ID | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48018-6 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | CodeableConcept | If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used. Binding: HGNC (extensible): HGNC: Human Gene Nomenclature Committee | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:cytogenetic-location | Σ | 0..* | BackboneElement | Cytogenetic (chromosome) location | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48001-2 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding: (unbound) (example): Binding not yet defined | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:ref-sequence-assembly | Σ | 0..* | BackboneElement | Human reference sequence assembly version | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 62374-4 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding: LOINC Answer List LL1040-6 (extensible): Human reference sequence NCBI build IDs | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:dna-chg | Σ | 0..1 | BackboneElement | DNA Change - Transcript (cHGVS) | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48004-6 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding: HGVS (required): HGVS: Sequence Variant Nomenclature from the Human Genome Variation Society | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:dna-chg-type | Σ | 0..1 | BackboneElement | DNA change type | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48019-4 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | CodeableConcept | Concepts in sequence ontology under SO:0002072 (see http://www.sequenceontology.org/browser/current_release/term/SO:0002072) Binding: DNA Change Type (extensible): DNA Change type values (Sequence Ontology) | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:functional-annotation | Σ | 0..* | BackboneElement | Functional Annotation | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: functional-annotation | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | CodeableConcept | Concepts in sequence ontology under SO:0001537 (see http://www.sequenceontology.org/browser/current_release/term/SO:0001537) Binding: Functional Annotation (extensible): Functional Annotation (Sequence Ontology) | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:variation-code | Σ | 0..1 | BackboneElement | Variation Code | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81252-9 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding: (unbound) (example): Binding not yet defined | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:dbSNP-id | Σ | 0..1 | BackboneElement | dbSNP ID | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81255-2 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding: (unbound) (example): Binding not yet defined | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:genomic-dna-chg | Σ | 0..1 | BackboneElement | DNA Change - Genomic (gHGVS) | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81290-9 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding: HGVS (required): HGVS: Sequence Variant Nomenclature from the Human Genome Variation Society | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:genomic-source-class | Σ | 0..1 | BackboneElement | Genomic source class | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48002-0 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | CodeableConcept | Germline | Somatic | Fetal | Likely germline | Likely somatic |Likely fetal | Unknown genomic origin | De novo Binding: LOINC Answer List LL378-1 (extensible): Genomic source class values | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:amino-acid-chg | Σ | 0..1 | BackboneElement | Amino acid change (pHGVS) | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48005-3 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding: HGVS (required): HGVS: Sequence Variant Nomenclature from the Human Genome Variation Society | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:amino-acid-chg-type | Σ | 0..1 | BackboneElement | Amino acid change type | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48006-1 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | CodeableConcept | Wild type | Deletion | Duplication | Frameshift | Initiating Methionine | Insertion | Insertion and Deletion | Missense | Silent | Stop Codon Mutation Binding: LOINC Answer List LL380-7 (required): Amino acid change type values | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:transcript-ref-seq | Σ | 0..1 | BackboneElement | Transcript reference sequence ID | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 51958-7 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding: (unbound) (example): Binding not yet defined | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:genomic-ref-seq | Σ | 0..1 | BackboneElement | Genomic reference sequence ID | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48013-7 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding: (unbound) (example): Binding not yet defined | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:sample-allelic-frequency | Σ | 0..1 | BackboneElement | Sample Allelic Frequency | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Sample Sample VAF Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81258-6 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | Quantity | Actual component result | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | |||||
| value | Σ | 1..1 | decimal | Numerical value (with implicit precision) | ||||
| comparator | ?!Σ | 0..1 | code | < | <= | >= | > - how to understand the value Binding: QuantityComparator (required): How the Quantity should be understood and represented. | ||||
| unit | Σ | 0..1 | string | Unit representation | ||||
| system | ΣC | 1..1 | uri | System that defines coded unit form Fixed Value: http://unitsofmeasure.org | ||||
| code | Σ | 0..1 | code | Coded form of the unit | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:allelic-read-depth | Σ | 0..* | BackboneElement | Allelic read depth | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 82121-5 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | Quantity | Actual component result | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:allelic-state | Σ | 0..1 | BackboneElement | Allelic state | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 53034-5 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | CodeableConcept | Heteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous Binding: LOINC Answer List LL381-5 (extensible): Allelic state type values | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:copy-number | Σ | 0..1 | BackboneElement | Genomic structural variant copy number | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 82155-3 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | C | 1..1 | Count | A measured or measurable amount | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:ref-allele | Σ | 0..1 | BackboneElement | Genomic ref allele | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 69547-8 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | string | Actual component result | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:alt-allele | Σ | 0..1 | BackboneElement | Genomic alt allele | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 69551-0 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | string | Actual component result | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:coordinate-system | Σ | 0..1 | BackboneElement | Coordinate System | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 92822-6 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | CodeableConcept | 0-based interval | 0-based character | 1-based character Binding: LOINC Answer List LL5323-2 (preferred): Base coordinate systems start and end measurements for variants | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:exact-start-end | Σ | 0..1 | BackboneElement | Exact start-end | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: exact-start-end | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | Range | Actual component result | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | |||||
| low | Σ | 1..1 | SimpleQuantity | Exact Start | ||||
| high | Σ | 0..1 | SimpleQuantity | Exact End | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:variant-length | Σ | 0..1 | BackboneElement | Structural variant length | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81300-6 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | C | 1..1 | Count | A measured or measurable amount | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:outer-start-end | Σ | 0..1 | BackboneElement | Variant outer start and end | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: outer-start-end | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | Range | Actual component result | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | |||||
| low | Σ | 1..1 | SimpleQuantity | Low limit | ||||
| high | Σ | 1..1 | SimpleQuantity | High limit | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:inner-start-end | Σ | 0..1 | BackboneElement | Variant inner start and end | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: inner-start-end | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | Range | Actual component result | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | |||||
| low | Σ | 1..1 | SimpleQuantity | Low limit | ||||
| high | Σ | 1..1 | SimpleQuantity | High limit | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:chromosome-copy-number-change-type | Σ | 0..1 | BackboneElement | Chromosome copy number change type | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 62378-5 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | CodeableConcept | Copy number gain | Copy number loss Binding: LOINC Answer List LL1041-4 (required): Copy Number Change Types | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:arrCGH-ratio | Σ | 0..1 | BackboneElement | Structural variant reported arrCGH [Ratio] | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81299-0 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | C | 1..1 | SimpleQuantity | A fixed quantity (no comparator) | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:complex-var-type | Σ | 0..1 | BackboneElement | Complex variant type | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81263-6 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | CodeableConcept | Compound heterozygous | Double heterozygous | Haplotype | Hemizygous Binding: LOINC Answer List LL3999-1 (required): Complex variant type | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:cytogenomic-nomenclature | Σ | 0..1 | BackboneElement | Cytogenomic Nomenclature | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Variant ISCN Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81291-7 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding: (unbound) (example): Binding not yet defined | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:variant-inheritance | Σ | 0..1 | BackboneElement | Variant Inheritance | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: variant-inheritance | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding: Variant Inheritance (extensible): Variant Inheritance (Sequence Ontology) | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:actionability | Σ | 0..1 | BackboneElement | Conclusion of the clinicians wether the variant is actionable or not during the Molecular Tumor Board | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 93348-1 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| Slices for value[x] | Σ | 0..1 | boolean | Actual component result Slice: Unordered, Closed by type:$this | ||||
| value[x]:valueBoolean | Σ | 0..1 | boolean | Actual component result | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:proposed-for-orientation | Σ | 0..1 | BackboneElement | Is the ClinicalTumorBoardConclusion used to orient the treatment decision ? | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/umls | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: C0449889 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| Slices for value[x] | Σ | 0..1 | boolean | Actual component result Slice: Unordered, Closed by type:$this | ||||
| value[x]:valueBoolean | Σ | 0..1 | boolean | Actual component result | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:pathogenicity | Σ | 0..1 | BackboneElement | Conclusion of the biologist on the pathogenicity of the variant before the Molecular Tumor Board | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 74019-1 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| Slices for value[x] | Σ | 0..1 | CodeableConcept | Actual component result Slice: Unordered, Closed by type:$this Binding: Pathogenicity Value Set (required) | ||||
| value[x]:valueCodeableConcept | Σ | 0..1 | CodeableConcept | Actual component result | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:loss-of-heterozygosity | Σ | 0..1 | BackboneElement | Is the segment located in a region of loss of heterozygosity ? (can be independant from copy number information | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/umls | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: C1881449 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| Slices for value[x] | Σ | 0..1 | boolean | Actual component result Slice: Unordered, Closed by type:$this | ||||
| value[x]:valueBoolean | Σ | 0..1 | boolean | Actual component result | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:segment-intensity | Σ | 0..1 | BackboneElement | Intensity of the measured signal | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | id | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/umls | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: C2732930 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| Slices for value[x] | Σ | 0..1 | integer | Actual component result Slice: Unordered, Closed by type:$this | ||||
| value[x]:valueInteger | Σ | 0..1 | integer | Actual component result | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| Documentation for this format | ||||||||
| Path | Conformance | ValueSet / Code | ||||
| Observation.language | preferred | CommonLanguages
| ||||
| Observation.status | required | ObservationStatus | ||||
| Observation.category | preferred | Pattern: laboratory | ||||
| Observation.code | example | Pattern: LOINC code 69548-6 | ||||
| Observation.value[x] | required | LOINC LL1971-2 | ||||
| Observation.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.bodySite | example | SNOMEDCTBodyStructures | ||||
| Observation.method | extensible | LOINC LL4048-6 | ||||
| Observation.referenceRange.type | preferred | ObservationReferenceRangeMeaningCodes | ||||
| Observation.referenceRange.appliesTo | example | ObservationReferenceRangeAppliesToCodes | ||||
| Observation.component.code | example | LOINCCodes (a valid code from LOINC) | ||||
| Observation.component.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:gene-studied.code | example | Pattern: LOINC code 48018-6 | ||||
| Observation.component:gene-studied.value[x] | extensible | HGNC | ||||
| Observation.component:gene-studied.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:cytogenetic-location.code | example | Pattern: LOINC code 48001-2 | ||||
| Observation.component:cytogenetic-location.value[x] | example | |||||
| Observation.component:cytogenetic-location.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:ref-sequence-assembly.code | example | Pattern: LOINC code 62374-4 | ||||
| Observation.component:ref-sequence-assembly.value[x] | extensible | LOINC LL1040-6 | ||||
| Observation.component:ref-sequence-assembly.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:dna-chg.code | example | Pattern: LOINC code 48004-6 | ||||
| Observation.component:dna-chg.value[x] | required | HGVS | ||||
| Observation.component:dna-chg.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:dna-chg-type.code | example | Pattern: LOINC code 48019-4 | ||||
| Observation.component:dna-chg-type.value[x] | extensible | DnaChangeType | ||||
| Observation.component:dna-chg-type.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:functional-annotation.code | example | Pattern: functional-annotation | ||||
| Observation.component:functional-annotation.value[x] | extensible | FunctionalAnnotation | ||||
| Observation.component:functional-annotation.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:variation-code.code | example | Pattern: LOINC code 81252-9 | ||||
| Observation.component:variation-code.value[x] | example | |||||
| Observation.component:variation-code.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:dbSNP-id.code | example | Pattern: LOINC code 81255-2 | ||||
| Observation.component:dbSNP-id.value[x] | example | |||||
| Observation.component:dbSNP-id.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:genomic-dna-chg.code | example | Pattern: LOINC code 81290-9 | ||||
| Observation.component:genomic-dna-chg.value[x] | required | HGVS | ||||
| Observation.component:genomic-dna-chg.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:genomic-source-class.code | example | Pattern: LOINC code 48002-0 | ||||
| Observation.component:genomic-source-class.value[x] | extensible | LOINC LL378-1 | ||||
| Observation.component:genomic-source-class.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:amino-acid-chg.code | example | Pattern: LOINC code 48005-3 | ||||
| Observation.component:amino-acid-chg.value[x] | required | HGVS | ||||
| Observation.component:amino-acid-chg.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:amino-acid-chg-type.code | example | Pattern: LOINC code 48006-1 | ||||
| Observation.component:amino-acid-chg-type.value[x] | required | LOINC LL380-7 | ||||
| Observation.component:amino-acid-chg-type.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:transcript-ref-seq.code | example | Pattern: LOINC code 51958-7 | ||||
| Observation.component:transcript-ref-seq.value[x] | example | |||||
| Observation.component:transcript-ref-seq.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:genomic-ref-seq.code | example | Pattern: LOINC code 48013-7 | ||||
| Observation.component:genomic-ref-seq.value[x] | example | |||||
| Observation.component:genomic-ref-seq.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:sample-allelic-frequency.code | example | Pattern: LOINC code 81258-6 | ||||
| Observation.component:sample-allelic-frequency.value[x].comparator | required | QuantityComparator | ||||
| Observation.component:sample-allelic-frequency.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:allelic-read-depth.code | example | Pattern: LOINC code 82121-5 | ||||
| Observation.component:allelic-read-depth.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:allelic-state.code | example | Pattern: LOINC code 53034-5 | ||||
| Observation.component:allelic-state.value[x] | extensible | LOINC LL381-5 | ||||
| Observation.component:allelic-state.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:copy-number.code | example | Pattern: LOINC code 82155-3 | ||||
| Observation.component:copy-number.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:ref-allele.code | example | Pattern: LOINC code 69547-8 | ||||
| Observation.component:ref-allele.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:alt-allele.code | example | Pattern: LOINC code 69551-0 | ||||
| Observation.component:alt-allele.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:coordinate-system.code | example | Pattern: LOINC code 92822-6 | ||||
| Observation.component:coordinate-system.value[x] | preferred | LOINC LL5323-2 | ||||
| Observation.component:coordinate-system.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:exact-start-end.code | example | Pattern: exact-start-end | ||||
| Observation.component:exact-start-end.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:variant-length.code | example | Pattern: LOINC code 81300-6 | ||||
| Observation.component:variant-length.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:outer-start-end.code | example | Pattern: outer-start-end | ||||
| Observation.component:outer-start-end.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:inner-start-end.code | example | Pattern: inner-start-end | ||||
| Observation.component:inner-start-end.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:chromosome-copy-number-change-type.code | example | Pattern: LOINC code 62378-5 | ||||
| Observation.component:chromosome-copy-number-change-type.value[x] | required | LOINC LL1041-4 | ||||
| Observation.component:chromosome-copy-number-change-type.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:arrCGH-ratio.code | example | Pattern: LOINC code 81299-0 | ||||
| Observation.component:arrCGH-ratio.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:complex-var-type.code | example | Pattern: LOINC code 81263-6 | ||||
| Observation.component:complex-var-type.value[x] | required | LOINC LL3999-1 | ||||
| Observation.component:complex-var-type.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:cytogenomic-nomenclature.code | example | Pattern: LOINC code 81291-7 | ||||
| Observation.component:cytogenomic-nomenclature.value[x] | example | |||||
| Observation.component:cytogenomic-nomenclature.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:variant-inheritance.code | example | Pattern: variant-inheritance | ||||
| Observation.component:variant-inheritance.value[x] | extensible | VariantInheritance | ||||
| Observation.component:variant-inheritance.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:actionability.code | example | Pattern: LOINC code 93348-1 | ||||
| Observation.component:actionability.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:proposed-for-orientation.code | example | Pattern: C0449889 | ||||
| Observation.component:proposed-for-orientation.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:pathogenicity.code | example | Pattern: LOINC code 74019-1 | ||||
| Observation.component:pathogenicity.value[x] | required | Pathogenicity | ||||
| Observation.component:pathogenicity.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:loss-of-heterozygosity.code | example | Pattern: C1881449 | ||||
| Observation.component:loss-of-heterozygosity.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:segment-intensity.code | example | Pattern: C2732930 | ||||
| Observation.component:segment-intensity.dataAbsentReason | extensible | DataAbsentReason |
This structure is derived from Variant
Summary
Mandatory: 2 elements (4 nested mandatory elements)
Structures
This structure refers to these other structures:
Slices
This structure defines the following Slices:
Other representations of profile: CSV, Excel, Schematron
IG © 2020+ Arkhn. Package arkhn.fhir.uv.osiris#2.1.0 based on FHIR 4.0.1. Generated 2023-04-10
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